Multipole ion guide ion trap mass spectrometry with MS/MSN analysis

ABSTRACT

A method includes directing ions from an atmospheric pressure ion source to a first ion guide; directing ions in the first ion guide to a second ion guide, the second ion guide being a multipole ion guide extending along an axis; periodically directing ions along the axis; receiving at least some of the ions in a time-of-flight analyzer; accelerating the ions in the time-of-flight mass analyzer orthogonal to the axis; and detecting the accelerated ions.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.09/901,428, filed Jul. 9, 2001, which is a continuation of U.S. patentapplication Ser. No. 08/694,542, filed Aug. 8, 1996, now U.S. Pat. No.6,011,259, issued on Jan. 4, 2000, which claims priority to ProvisionalApplication No. 60/002,117, filed Aug. 10, 1995.

U.S. patent application Ser. No. 09/901,428 is also a continuation ofU.S. patent application Ser. No. 09/676,124, filed Sep. 29, 2000, whichis a continuation of U.S. patent application Ser. No. 09/373,337, filedAug. 12, 1999, now U.S. Pat. No. 6,188,066, issued on Feb. 13, 2001,which is a continuation of U.S. patent application Ser. No. 08/794,970,filed Feb. 5, 1997, now U.S. Pat. No. 5,962,851 issued on Oct. 5, 1999,which is a continuation of U.S. patent application Ser. No. 08/645,826,filed May 14, 1996, now U.S. Pat. No. 5,652,427 issued on Jul. 29, 1997,which is a continuation of U.S. patent application Ser. No. 08/202,505,filed Feb. 28, 1994, now abandoned. U.S. patent application Ser. No.09/901,428 is also a continuation of U.S. patent application Ser. No.09/808,468, filed Mar. 14, 2001, now U.S. Pat. No. 7,019,285 issued onMar. 28, 2006, which is a continuation of U.S. patent application Ser.No. 09/448,857, filed Nov. 23, 1999, now abandoned, which is acontinuation of U.S. patent application Ser. No. 08/971,521, filed Nov.17, 1997, now U.S. Pat. No. 6,020,586 issued on Feb. 1, 2000, which is acontinuation of U.S. patent application Ser. No. 08/689,459, filed Aug.9, 1996, now U.S. Pat. No. 5,689,111 issued on Nov. 18, 1997, whichclaims priority to Provisional Application No. 60/002,118, filed Aug.10, 1995 and Provisional Application No. 60/002,122, filed Aug. 10,1995.

FIELD OF INVENTION

The invention relates to the field of mass analysis and the apparatusand methods used in analyzing chemical species. It is a continuing goalin the field of chemical and mass analysis to improve the performance ofmass analyzers and include more functional capability within a giveninstrument while reducing the instrument size, cost and complexity. Theinvention allows single or multiple mass selection, and fragmentationsteps (MS/MS^(n)) in Time-Of-Flight (TOF) mass analyzers by including amultipole ion guide in the ion flight path between the ion source andthe mass analyzer. Multipole ion guides have been used in mass analyzerswith Atmospheric Pressure Ion Sources (API) to improve ion transmissionperformance as is described in U.S. Pat. Nos. 4,963,736 and 5,179,278.In particular, the use of a multipole ion guide has been shown toimprove the performance of mass analyzers with API sources such asElectrospray (ES) and Atmospheric Pressure Chemical Ionization (APCI).MS/MS^(n) functional capability described herein as part of theinvention can be achieved with a minimum increase to System cost, sizeor complexity. API ion source types have been successfully used ininterfacing mass spectrometers to liquid separation systems such asLiquid Chromatography (LC) and Capillary Electrophoresis (CE). Theinvention will enable the TOF mass analyzer to perform an array of massand fragmentation analytical functions in a chemical analysis even whileon-line with separation systems. One aspect of the invention which usesa Time-Of-Flight mass analyzer is that the instrument is capable ofrapid full m/z range data acquisition speeds. MS and MS/MS^(n) analysisas described by the invention can be performed on line even with fastseparation systems such as perfusion LC and CE.

BACKGROUND OF THE INVENTION

The fragmentation of ions and subsequent mass analysis of the fragmentshas become a powerful technique used in chemical analysis. As theperformance improves and the capability of mass analyzers increases, theinstrumentation has been applied to a wider range of analytical methods.The mass analyzer has become a primary tool in the detection,identification and structural determination of chemical samples. Theinvention is an apparatus with means for incorporating single andmultiple step mass selection and ion fragmentation capability with TOFmass analysis. This is accomplished by using at least one multipole ionguide for ion transmission or trapping along with fragmentation of ionswithin the multipole ion guide internal volume by collisional induceddissociation. The invention can be configured with orthogonal andcoaxial pulsing TOF mass analyzers.

Ion fragmentation caused by Collisional Induced Dissociation (CID) of anion with neutral background gas has been a technique used in massspectrometry for some time. The CID step may or may not be accompaniedby a mass selection step. Often mass to charge (m/z) selection is usedprior to ion fragmentation using CID so that the resulting fragment ionscan be more readily identified as having been produced fromfragmentation of a given selected parent ion. If more than one parention undergoes fragmentation simultaneously then it may be difficult toidentify which fragment ions have been generated from which parent ionsin the resulting mass spectrum. The mass selection, fragmentation andsubsequent mass analysis steps can be achieved with multiple massanalyzers used in series or with ion trapping devices which include massanalysis capability. Multiple mass analyzers, such as triplequadrupoles, which are used to achieve selective CID collision have beencommercially available for some time and hence the term MS/MS has becomecommonly used to mean a mass selection step followed by and ionfragmentation step, followed by a mass analysis step of the fragmentions. The term MS/MS^(n) has come to mean multiple mass selection andfragmentation steps leading to one or more mass spectrum which may beacquired at each step or at the end of the last fragmentation step. In apreferred embodiment of the invention, a multipole ion guide isincorporated into an API TOF mass analyzer with orthogonal pulsing ofthe primary ion beam into the flight tube. Alternatively an axialcollinear TOF pulsing geometry can also be configured. The multipole ionguide is located in the second vacuum pumping stage just downstream ofthe skimmer and may be configured to end in vacuum pumping stage two orextend continuously into one or more additional vacuum pumping stages.Such multipole ion guides are disclosed in prior U.S. patent applicationSer. Nos. 08/641,628 (filed May 2, 1996) and 08/208,632 (filed Mar. 8,1994), the disclosures of which are hereby incorporated herein byreference. The multipole ion guide can be operated in a manner totransmit ions which are delivered into the ion guide entrance from theAPI source through the skimmer and direct them into the pulsing regionof the TOF mass analyzer. Alternatively, the ion multipole ion guide canbe operated in a manner where the ions are trapped within the ion guideinternal volume which is bounded by the evenly spaced rods or poles ofthe ion guide before being transmitted to pulsing region of the TOE massanalyzer. In either ion transmission or trapping mode of operation, thevoltages applied to the ion guide poles can lie set to transmit or trapa narrow m/z range of ions and cause fragmentation of selected m/z ionsby CID of the ions with the background gas.

Multipole ion guides can be configured with four (quadrupole), six(hexapole), eight (octapole) or more rods or poles with each rod equallyspaced at a common radius from the centerline and with all rodspositioned in a parallel manner. Ions with m/z values which fall withinthe ion guide stability window established by the applied voltages, havestable trajectories within the ion guide internal volume bounded by theparallel evenly spaced rods. In conventional multipole ion guideoperation, with no ion resonant frequency component added, every otherpole or rod has the same voltage applied and each adjacent pole has thesame amplitude voltage but the opposite polarity applied. Multipole ionguides with higher rod numbers have a larger ion acceptance area and canin a stable trajectory transmit a wider range of m/z valuessimultaneously. Higher resolving power can be achieved for multipole ionguides with a lower number of poles when operating the ion guide inmanner where narrow m/z selection is desired. For example, a narrow m/zwindow of stable ion transmission is more readily achievable using aquadrupole ion guide when compared with hexapole or octapole ion guideperformance. As narrow m/z range mass selection is desirable for someMS/MS^(n) applications, a quadrupole ion guide will be included in apreferred embodiment of the invention. For applications where narrow m/zrange selection is not required, a hexapole or octapole may bepreferred. This could be the case where a front end separation systemsuch as LC or CE has been employed to achieve component separationbefore the sample is introduced into the API TOF instrument. If thecomponents are delivered individually to the API source subsequent massselection may not be required before the fragmentation step.

AC and DC voltage components are applied to the parallel poles of aquadrupole ion guide in a manner which causes a stable or unstable iontrajectory for specific m/z values as an ion traverses the length of theion guide internal volume. In Cartesian coordinates, the equations ofmotion for an ion traversing the electric fields applied to a quadrupoleion guide as reported by Dawson P. H. (“Quadrupole Mass Spectrometry andits applications”, Elsevier Scientific Publishing Co., New York, 1976)are described by the Mathieu Equations;

$\begin{matrix}{{{\frac{\mathbb{d}^{2}u}{\mathbb{d}\;\xi^{2}} + {\left( {a_{u} - {2\; q_{u}\cos\; 2\xi}} \right)u}} = 0}{and}} & (1) \\{\frac{\mathbb{d}^{2}z}{\mathbb{d}^{2}\xi^{2}} = 0} & (2)\end{matrix}$

The z coordinate is along the multipole in guide axis, and the x and yaxis describe the radial plane with the centerline of two opposing poleslying on the y axis and the centerline of the remaining two opposingpoles lying on the x axis. A cross section of the quadrupole with roundrods is diagrammed in FIG. 10. The centerline 109 of quadrupole 108 liesat the intersection of the x and y axis. The centerline of rods 104 and106 lie along the x axis and the centerline of rods 105 and 107 liealong the y axis. All rods have the same radius and all rod centerlineslie on a common radius from quadrupole centerline 109. The distance fromcenterline 109 to the intersection point of a rod surface is defined tobe r₀. In the quadrupole field created by the voltages applied to theion guide rods, the ion motion along each of the three axis isindependent, so u is either x or y and a_(u) and q_(u) are defined bythe relations;

$\begin{matrix}{a_{u} = {a_{x} = {{- a_{y}} = {\frac{4\; U}{\frac{m}{z}\omega^{2}r_{0}^{2}}{and}}}}} & (3) \\{q_{u} = {q_{x} = {{- q_{y}} = {\frac{2\; V}{\frac{m}{z}\omega^{2}r_{0}^{2}}.}}}} & (4)\end{matrix}$

U is the DC voltage component amplitude, V is the primary AC or RFcomponent frequency amplitude, m/z is the ion mass to charge, ω=2πf isthe angular frequency of the primary AC voltage component, r₀ is theradial distance from the ion guide assembly centerline to the nearestinside rod surface and ξ=ωt/2=πft where t is time in seconds and f isthe primary AC voltage frequency. The solution of equation 1 can beexpressed in terms of variables a, q and μ where μ is a purely imaginarynumber defined as μ=iβ. The variable β is related to the frequencycomponents of the ion motion in the x and y directions as the iontraverses or is trapped in the ion guide. The fundamental frequency ofthe ion motion is given by the relationω₀=βω/2  (5).

The lower and upper limits of ion stability are the boundaries where β=0and 1 respectively as shown in the x and y ion movement overlappingstability region 102 diagrammed in FIG. 9. When the AC voltage componentis applied to the ion guide poles with relative rod to rod DC voltagecomponent set to zero the ion guide operates along the a=0 axis 101 onthe stability diagram 102 in FIG. 9. For the case of a=0 operation whereβ_(y) β_(x), Reinsfelder and Denton [International J. of Mass Spectromand Ion Physics, 37 (1981), 241] have shown that q can expressed as afunction of β by the relationq=2β(1−0.375β²)  (6).

Combining equations 4, 5 and 6, the motion of each m/z value traversingthe ion guide has a primary resonant frequency in the a=0 (RF only)operating mode predicted by the relation

$\begin{matrix}{\frac{m}{z} = {\frac{V}{r_{0}^{2}\omega_{0}{\omega\left\lbrack {1 - {1.5\left( \frac{\omega_{0}}{\omega} \right)^{2}}} \right\rbrack}} = {\frac{V\;\omega}{r_{0}^{2}{\omega_{0}\left\lbrack {\omega^{2} - {\frac{3}{2}\omega_{0}^{2}}} \right\rbrack}}.}}} & (7)\end{matrix}$

Watson et. al, [International, J. of Mass Spectrom and Ion Processes, 93(1989) 225] have reported that a resonant frequency applied as asupplementary lower frequency AC voltage to two opposing or all fourmultipole rods can successfully reject a narrow m/z range of ions evenwith a single pass through the quadrupole ion guide operated in the RFonly mode. The resonant frequency for a given m/z value may differslightly from the predicted value given by expression 7. This is due inpart to entrance effects on ion trajectory, distortions in the electricfields due to rod tolerances and round rod shapes typically used inquadrupole ion guide construction instead of hyperbolic rod crosssections. With the ion motion in a quadrupole ion guide readilycontrolled by applied AC and DC voltage components, a number of methodscan be employed to achieve m/z selection and CID fragmentation steps. Asis shown in formulas 1 and 2, the z or axial component of ion motion isindependent of the ion motion in the radial direction in a multipole ionguide parallel rod quadrupole field. Consequently, similar functions canbe achieved on a single pass or in ion trapping mode. The ability of theTOF mass analyzer to acquire full mass spectra at a rapid rate offersseveral advantages over other mass analyzer types when it is combinedwith quadrupole ion guide which can be run in mass selection and ionfragmentation operating modes.

Several techniques to achieve specific m/z range selection are possiblewhen operating with quadrupole ion guides. One technique method is toapply AC and DC voltage component values which fall near the top 100 ofstability region 102 as shown in FIG. 9. The a and q values resultingfrom the applied AC and DC voltage components will fall in the area 100near the top of stability diagram 102, that is the point where q=0.706and a=0.237, for a select range of m/z values. The closer the a and qvalues are to the tip 100 of stability diagram 102, 0.237 and 0.706respectively for a given m/z value, the higher the resolution for thatselected m/z value and hence the narrower the range of m/z values thathave a stable trajectory and can pass through or remain trapped in thequadrupole ion guide. A single range of m/z values can be selected inthis manner with the range being determined by values of a and qselected which fall within stability diagram 102 shown in FIG. 9.Sensitivity may be reduced when operating the quadrupole at higherresolution. Dawson has shown that the closer the quadrupole is operatedto the apex region 100 of stability diagram 102, the smaller theeffective quadrupole ion entrance aperture becomes. This mass selectionoperating method has the characteristic that as resolution increases theuseable ion entrance aperture decreases, potentially reducingsensitivity. A second technique described by Langmuir in U.S. Pat. No.3,334,225 and later Douglas in U.S. Pat. No. 5,179,278, provides analternative means of achieving mass selection by applying an additionalbroad band resonant ion excitation frequency voltage added to the ACvoltage component applied two opposing or all four rods while filteringout the resonant frequency for the range of m/z values selected. Ion m/zvalues which correspond to the applied resonant frequency range are gaintranslational energy in the radial direction of motion and are ejectedradially from the quadrupole ion guide. DC voltage components can beadded to the rods as well to cut off the high and low m/z values whichmay fall beyond the applied resonant frequency range. Kelly, in U.S.Pat. No. 5,345,078 describes a similar mass selection technique whilestoring ions in a three dimensional ion trap. This notch filter massselection can be used to trap or pass more than one range of m/z valuesin the quadrupole ion guide. Using inverse Fourier Transforms applied todefine the signal output of waveform generators, several notches can beprogrammed into the auxiliary resonant frequency waveform added to thequadrupole rods resulting in the simultaneous selection of multiple m/zvalues. A third mass selection technique is to trap a wide range of m/zvalues ions in a quadrupole ion guide at low resolution and then applyAC and DC voltage components to the rods improving resolution. andrejecting unwanted m/z values above and below the selected m/z range.Alternatively, ions can be trapped in the quadruple operating in the RFonly mode along a=0 line 101 in FIG. 9 and the AC voltage amplitudecomponent can be varied such that ions above and below the desired m/zvalue are rejected from the quadrupole ion guide while those or interestremain trapped.

The m/z selection step is followed by an ion fragmentation step inMS/MS^(n) analysis. A multipole ion guide located in the second vacuumpumping stage of an API MS system can operate effectively in backgroundpressures as high as 10⁻³ to 10⁻² torr range. Operation of a multipoleion guide in higher pressure vacuum regions for transmitting ions froman API source to an mass analyzer was described by C. Whitehouse et. al,in a paper presented at the 12 Montreux Liquid Chromatography and MassSpectrometry Symposium in Hilton Head, S.C., November 1995. Performanceof ion guides incorporated into API/MS instruments which extend intomore than one vacuum pumping stage were described. Ion guides wereoperated with little or no loss in ion transmission efficiency in vacuumbackground pressures as high as 180 millitorr over a portion of the ionguide length. The higher background pressure inside the ion guideinternal volume caused a collisional damping of the ion energy for ionstraversing the ion guide length and effectively increased the ion guideentrance aperture, D. Douglas et, al, in U.S. Pat. No. 4,963,736reported increased ion transmission efficiencies when a quadrupole ionguide operated in RF only mode and located in single vacuum pumpingstage in an API/quadrupole mass analyzer was run with backgroundpressures between 4 to 10 millitorr. When higher pressures aremaintained over all or a portion of the multipole ion guide length, ionswithin the ion guide internal volume can be fragmented by collisioninduced dissociation with the neutral background molecules. Douglas('278) describes applying a resonant frequency of low amplitude to therods of a quadrupole ion guide to fragment mass selected trapped ions byCID with the neutral background gas before conducting a mass analysisstep with a three dimensional quadrupole ion trap. At least twoadditional techniques may be used to cause fragmentation of ions in amultipole ion guide where the pressure along portion the ion guidelength is greater than 5×10⁻⁴ torr. In the first alternative technique,trapped ions are initially released from the ion guide exit end bychanging the appropriate ion guide and electrostatic lens voltages. Theenergy of the released ions is then raised by changing the voltageapplied to two electrostatic lenses as the ions traverse the gap betweenthese lenses. The ions with raised potential are then accelerated backinto the ion guide exit where ion fragmentation can occur as ionscollide with neutral background gas as the ions traverse the ion guidevolume moving toward the ion guide entrance end. Higher energy CID canbe achieved with this ion fragmentation technique. The second method isto fill the multipole trap to a level where fragmentation of the trappedion occurs. Techniques which use CID of ions within the multipole ionguide internal volume in an API/TOF mass analyzer will described in moredetail below.

The invention which includes a multipole ion guide or trap in an API/TOFmass analyzer allows several performance advantages and a more diverserange of operating functions when compared with other API/ion trap/massanalyzer types. S. Michael et, al. (Anal. Chem, 65 (1993), 2614)describes the using a three dimensional quadrupole ion trap to trap ionsdelivered from an Electrospray ion source in a TOF mass analyzerapparatus. The trapped ions are then pulsed from the three dimensionalquadruple ion trap linearly down the flight tube of a TOF mass analyzer.The three dimensional ion trap can be used for mass selection and CIDfragmentation as well prior to TOF mass analysis. A multipole ion guidefunctionally is the reciprocal of the three dimensional quadrupole iontrap (3D ion trap) and as such the multipole ion guide is morecompatible with TOF operation when it is incorporated into a TOF massanalyzer. When trapping ions, both the multipole ion guide and the 3Dion trap must have voltages applied which will allow stable ion motionfor the trapped m/z range of interest. For an ion to leave a 3D ion trapit must be forced into an unstable trajectory. For an ion to leave theend of a multipole ion guide it must have a stable ion trajectory. Thus,a multipole ion guide can be operated in either a trapping or nontrapping ion transfer mode when delivering ions to the pulsing region ofa TOF analyzer. A 3D ion trap can not be operated in a non trapping modein the configuration described by Michael et. al. When an orthogonalpulsing TOF geometry is used; ions exiting the multipole ion guide arepulsed into the TOF flight tube in an independent step. Multipole ionguides as configured in the invention can have higher trappingefficiencies than 3D traps and of significance in terms of performance,ions can be continuously entering the multipole ion guide even in ionstorage and release operating mode. The incoming ion beam is generallyturned off with 3D ion trap is mass scanning, collisionally coolingtrapped ions, fragmenting ions or releasing ions from the trap. Thisreduces duty cycle and sensitivity with TOF mass analysis. All ions mustbe pulsed from the 3D ion trap into the TOF flight tube for massanalysis whereas only a portion of the ions need to be pulsed from amultipole ion guide for TOF analysis. Due to a significantly largerinternal volume, an ion guide can trap a greater number of ions than a3D ion trap. The 3D ion trap must have an internal pressure in the 10⁻³torr range to increase ion trapping efficiency and to enable collisionalcooling of the trapped ions. The trap is adjacent to the TOF flight tubewhich must be held at pressures below 10⁻⁶ torr to avoid ion collisionswith the background gas during the flight time. As such, the 3D trapinternal higher pressure region is incompatible with the low pressureflight tube requirements. A multipole ion guide which extends into morethan one vacuum stage or a series of ion guides located in sequentialvacuum stages have the advantage being able to deliver ions into a lowpressure vacuum region before the ions enter the flight tube vacuumpumping stage.

The TOF mass analyzer has very different interfacing requirements thatof a 3D trap mass analyzer. Douglas ('278) describes a multipole ionguide operated as with an API/3D ion trap mass analyzer where all ionstrapped in the multipole ion guide are pulsed into 3D ion trap. Theprecise timing of the ion release pulse from the multipole ion guideinto the 3D ion trap does fundamentally affect system performance in theinstrument described. The timing, energy and shape of the ion pulsereleased from the multipole ion guide into the pulsing region of a TOFmass analyzer is critical to the mass spectrometer performance. Specificsequence control of the ion release function in a TOF analyzer providesimproved duty cycle performance when compared 3D ion trap mass analyzerperformance as will be described in more detail-below. Douglas ('278)describes performing trapping and a fragmentation step followed by fullemptying of the ion guide into the 3D ion trap for mass analysis, asequence which takes at least 0.12 seconds to perform. Unlike the 3D iontrap, the TOF mass analyzer conducts a mass analysis without scanning.Consequently, the TOF mass analyzer can perform large m/z range massanalysis at a rate greater than 20,000 times per second withoutcompromising resolution or mass accuracy. The TOF can perform a largem/z range mass analysis a rate which is faster than the time it takes anion to traverse the multipole ion guide length. A more diverse and awider range of data acquisition functions can be performed to achieveMS/MS^(n) analysis when using a TOF mass analyzer compared with othermass analyzer types. The present invention as described in more detailbelow, describes multipole ion guide TOF functions which not onlyprovide MS/MS^(n) analysis but can also include TOF mass analysis ateach MS/MS step.

SUMMARY OF THE INVENTION

In accordance with the present invention, a linear multipole ion guideis incorporated into an Atmospheric Pressure Ionization Source TOF massanalyzer. The multipole ion guide can be operated in a manner whichenables MS/MS^(n) performance capability in an API/TOF mass analyzer.The multipole ion guide is configured to operate with m/z rangeselection, trapping and subsequent ion fragmentation using CID withinthe multipole ion guide. Parent ions and multiple generations offragment ions formed within the ion guide are subsequentlyTime-Of-Flight mass analyzed. The multipole ion guide as configured inthe invention is positioned between the API source and the TOF flighttube. In a preferred embodiment of the invention, a linear multipole ionguide is incorporated into a Time-Of-Flight mass analyzer apparatus. Themultipole ion guide is located in the vacuum pumping stage or stagesbetween the ion source, specifically downstream of the orifice intovacuum from an Atmospheric Pressure Ion (API) source, and the pulsingregion of the TOF mass analyzer. The ion guide serves as an efficientmeans for transferring ions through one or more vacuum pumping stagesbetween the API source free jet expansion and the TOF ion beam pulsinglenses. When transporting ions in a continuous beam, the multipole ionguide is usually operated in an RF only mode which allows the stabletransport of a wide range of m/z values through the ion guide whileholding the electrostatic entrance and exit lens potentials at aconstant value to optimize focusing of the primary beam into the TOFpulsing region. In the present invention the multipole ion guide isoperated in both a non trapping mode and in an ion storage or trap modewith ions pulsed from the ion guide into the TOF analyzer pulsingregion. This pulsed ion extraction from the exit of the multipole ionguide can be selected to occur with or without interruption of the ionaccumulation process within the multipole ion guide. The multipole ionguide operated in the ion storage or trap mode can be configured fordelivering ions to either a collinear or an orthogonal pulsing TOFgeometry where the ions are subsequently pulsed into the TOF massanalyzer flight tube.

The invention includes the operation of the multipole ion guide toselectively trap, fragment and transmit ions to the pulsing region of aTOF mass analyzer to achieve MS/MS^(n) functionality in a TOF massanalyzer apparatus interfaced to an API source. The electrical voltagesapplied to the rods of the multipole ion guide including AC and DCcomponents are adjustable such that a selected range of ion m/z valueshave stable trajectories within the ion guide electrical field.Electrostatic lenses are configured on the multipole ion guide entranceand exit ends such that voltages applied to these lenses allow eitherion transmission through the multipole ion guide or trapping of ionswithin the ion guide. The relative electrostatic lens potentialsupstream of the multipole ion guide can be set to transmit or cut offthe primary ion beam to the ion guide as desired during ion guidetrapping and CID steps. A specific m/z value or range of m/z values canbe transmitted or trapped with the multipole ion guide by applying theappropriate AC and DC voltages on the multipole rods. This function willbe referred to as m/z or mass selection. It is often preferable toperform m/z selection prior to an ion fragmentation step to allowdefinitive assignment of fragment ions to a specific parent ion. Theinvention includes the ability to conduct MS/MS analysis in anAPI/multipole on guide/TOF mass analyzer, where the multipole ion guidefirst performs a mass selection step and a subsequent fragmentationstep. The resulting ion population is then released from the multipoleion guide into the TOF mass analyzer pulsing region from which the ionsare mass analyzed when pulsed down the TOF flight tube. The multipoleion guide mass selection and ion fragmentation steps are achieved byapplying a voltages to the multipole ion guide rods and the entrance andexit electrostatic lenses in a stepwise process. In one embodiment ofthe invention the ion beam is transmitted into the multipole ion guidewhich is operated in a mass selective trapping mode. When the multipoleion guide trap has been filled to the desired level, all or a portion ofthe ions in the linear multipole ion guide trap are fragmented usingcollisional induced dissociation. All or a portion of the trapped ionsare then transmitted to the pulsing region of the TOF mass analyzerwhere they are accelerated into the TOF flight tube and m/z analyzed.The mass selection, trapping and CID steps can be repeated in sequenceallowing MS/MS^(n) functional capability with the ability to perform TOFmass analysis at one or more MS/MS steps. The ion fragmentation step canbe performed in continuos transmission or trapping mode; with or withouta mass selection step. Due to the rapid mass analysis capability of theTOF, the ion guide can be operated in a trapping and fragmentation stepsequence without breaking the incoming ion stream.

The invention includes at least three methods to perform ionfragmentation with CID in the linear multipole ion guide. In addition,ion fragmentation can occur prior to the ion guide in the capillary toskimmer region. The first CID technique is to excite ions of selectedm/z values in the ion guide with a resonant frequency applied to the ionguide poles superimposed on the multipole ion guide rod's AC and DCelectrical components. The second CID method is to switch the voltageson the multipole ion guide exit lenses such that ions are released fromthe ion guide exit end, the ion potential is increased and ions areaccelerated back into the ion guide to collide with neutral gasmolecules present along the multipole ion guide length. The third methodis to fill the multipole ion guide with ions to a critical level suchthat CID occurs with the trapped ions. All or a portion of the trappedparent and fragment ions can be released from the multipole ion guideand mass analyzed with a TOF mass analyzer. Each of the three CIDmethods requires that the neutral gas pressure at some point along theion guide length be maintained high enough to cause collisional induceddissociation of ions within the ion guide.

In a preferred embodiment of the invention, a multipole ion guideextends into more than one vacuum pumping stage. The ion guide entranceis located just downstream of the skimmer orifice in a API source. Theneutral gas pressure along the length of a multipole ion guide whichextends through more than one vacuum pumping stage can vary by orders ofmagnitude with the region at the ion guide entrance having the highestpressure. This multipole ion guide geometry allows exposure of ions tohigher pressures for kinetic energy cooling or CID fragmentation yetions are delivered into a lower collision free vacuum pressure regionupstream of the TOF pulsing region without compromising the low vacuumpressure requirements on the TOF flight tube. Also, the variablepressure along the ion guide length allows higher collisional energiesto be attained for ions accelerated into the exit end of the ion guidethan can be achieved with resonant frequency excitation. Consequently, acontinuos range of low to high energy CID fragmentation of ions ispossible with the invention.

DESCRIPTION OF DRAWINGS

FIG. 1 is a diagram of a preferred embodiment of the invention with anElectrospray ion source, a multipole ion guide which extends into twovacuum pumping stages and a Time-Of-Flight mass analyzer with orthogonalpulsing and an ion reflector.

FIG. 2 is a diagram of the ion guide and TOF pulsing region of thepreferred embodiment diagrammed in FIG. 1 where a pulse of ions has beenreleased from the ions trapped in the multipole ion guide.

FIG. 3 is a diagram of the ion guide and TOF pulsing region of thepreferred embodiment diagrammed in FIG. 1 where the ions which havetraveled from the ion guide exit to the TOF pulsing region areorthogonally pulsed down the TOF flight tube.

FIG. 4 is a diagram of a second embodiment of the invention whichincludes two multipole ion guides each located in adjacent vacuumpumping stages in an API orthogonal pulsing TOF mass analyzer.

FIG. 5 is a diagram of a third embodiment of the invention where an APITOF mass analyzer with orthogonal pulsing includes a multipole ion guidelocated the second vacuum pumping stage of a three pumping stage system.

FIG. 6 is a diagram of a fourth embodiment of the invention whichincludes an Electrospray ion source, a multipole ion guide which extendsinto two vacuum pumping stages and a Time-Of-Flight mass analyzer with acollinear pulsing geometry and a linear flight tube.

FIG. 7 is a diagram of the ion guide and TOF pulsing region of theembodiment diagrammed in FIG. 6.

FIG. 8 shows the mass spectrum of the parent ion of Leucine Enkephalinand the mass spectra of the fragment ions from Leucine Enkephalinresulting from filling of the ion guide in a trap operating mode withtwo levels of capillary to skimmer voltages.

FIG. 9 is a Mathieu stability diagram near the origin for a quadrupoleion guide, showing the iso-β contours.

FIG. 10 is an end view of a quadrupole ion guide with round rods.

DESCRIPTION OF THE INVENTION

Atmospheric Pressure Ion sources interfaced to mass analyzers includeElectrospray, nebulizer assisted Electrospray, Atmospheric PressureChemical Ionization, Inductively Coupled Plasma (ICP) and Glow Dischargeion sources. Ions produced at or near atmospheric pressure by one ofthese ion source types are delivered to vacuum through a nozzle orcapillary orifice along with the carrier gas which was present in theatmospheric pressure source chamber. The gas exiting the orifice intovacuum forms a free jet expansion in the first vacuum pumping stage. Thevacuum stage partitions and ion optics downstream from the orifice intovacuum are designed to provide an efficient means of transporting ionsinto the mass analyzer with a minimum energy spread and angulardivergence while neutral background gas is pumped away. One or morevacuum pumping stages have been used with various API/MS designs. Massanalyzers such as TOF require that flight tube operating pressures be inthe low 10⁻⁶ to 10⁻⁷ torr range to avoid collisional scattering of ionsas they traverse the flight tube. Typically API/TOF mass spectrometerinstruments include three or more vacuum pumping stages to removebackground gas exiting from the API source orifice into vacuum.Multipole ion guides have been used to transport ions emerging from anAPI source through individual vacuum stages into an orthogonal TOF massanalyzer (Whitehouse et. al). The present invention includes a multipoleion guide incorporated in either a coaxial or orthogonally pulsedAPI/TOF mass analyzer instrument. This multipole ion guide can beoperated in either a mass filter, transmission, trapping or ionfragmentation mode to increase sensitivity and provide MS/MS^(n)capability with TOF analyzers.

FIG. 1 illustrates a preferred embodiment of the invention where amultipole ion guide extends continuously through two vacuum pumpingstages in an Electrospray TOF mass analyzer apparatus. In the embodimentshown, the TOF utilizes orthogonal pulsing of ions into the flight tubefor mass, analysis. Charged droplets are formed by the Electrospray ornebulization assisted Electrospray process from the liquid sampleintroduced into the Electrospray ion source 1 through tube 2. Thecharged liquid droplets are driven towards capillary entrance 6 againsta heated counter current drying gas 5 by the electrostatic fields in theElectrospray chamber. Ions are produced from the rapidly evaporatingcharged liquid droplets and a portion of these ions are enter capillaryorifice 8 and are swept into vacuum. Nozzles have also been used in APIsources as well to provide an orifice into vacuum. Capillary heater 9 islocated along a portion the length of capillary 7 to heat the gas andion mixture in capillary orifice 8 as it travels from atmosphericpressure into vacuum. The neutral carrier gas, usually nitrogen, forms asupersonic free jet expansion as it leaves capillary exit 12 and sweepsalong the entrained ions. Voltages are applied to the conductivecapillary exit 12 and skimmer 14 to focus ions through skimmer orifice13 and into multipole ion guide 16. The relative voltage betweencapillary exit 12 and skimmer 14 can be set to maximize ion transmissionthrough skimmer orifice 13 or can be increased to the point wherecollisional induced dissociation of ions traversing the gap betweencapillary exit 12 and skimmer opening 13 can occur. As the capillary toskimmer voltage is increased, ions are driven against the expandingneutral background gas increasing the internal energy of the ions. Aswill be described in a later section, increasing the internal energy ofions in the capillary skimmer region can be used to advantage whenfragmenting ions within the ion guide using CID of ions with thebackground gas in the multipole ion guide.

Typically the first vacuum pumping stage 10 is evacuated with a rotarypump which maintains background pressure ranging from 0.5 to 4 torr.With the capillary exit 12 to skimmer orifice 13 distance set typicallybetween 1 to 5 mm, a substantial neutral gas flux can pass throughskimmer orifice 13 into second vacuum stage 18. Ions exiting skimmerorifice 13 enter the electric field of ion guide 16 still experiencingsignificant numbers of collisions with the neutral background gas. Asthe ions continue to drift through the length of ion guide 16, theneutral gas is pumped away and the number of collisions with thebackground gas diminishes. Multipole ion guide 16 with rods 20 extendscontinuously from vacuum stage 18 into vacuum stage 19. Multipole ionguide 16 is supported by electrical insulator 22 and partition 21between vacuum stages 18 and 19. Multipole ion guide 16 can be aquadrupole, hexapole, octapole or can have higher numbers of rods. Forthe embodiment shown in FIG. 1, multipole ion guide 16 will be describedas a quadrupole hexapole with radial dimensions small enough to minimizeneutral gas conductance from vacuum stage 18 to vacuum stage 19. The r₀for such a quadrupole assembly can be as small as 1.25 mm. Multiplevacuum pumping stage hexapoles have been commercially available fromAnalytica of Branford. Inc. with an r₀ of approximately 1.25 mm.Hexapole ion guides which extend through more than one vacuum stage havebeen fabricated with rod diameters of 1 mm inside rod spacing of lessthan 2.5 mm. Ions exiting multipole ion guide 16 at exit end 24 arefocused by ion lenses 26, 27 and 28 into the orthogonal pulsing region30 defined by electrostatic lenses 34 and 35. Ions in primary ion beam48 are pulsed in an orthogonal direction into flight tube 42 throughgrids 35 and 36. Ion bunches pulsed through lenses or grids 35 and 36traverse TOF flight tube 42 in vacuum stage 37. Different m/z valuesarrive separated in time at detector 38 in ion reflector operating mode.Alternatively ions of different m/z values will arrive at differenttimes at detector 47 in a linear flight tube operating mode. Higherresolution can be achieved when ions accelerated from orthogonal pulsingregion 30 are reflected through single stage reflector lens assembly 46to detector 38. Two stage or gridless reflector assemblies can be usedas well. Ion flight path 45 can be varied for tuning purposes bychanging relative voltages on deflector lenses 44. Alternatively,pulsing the relative voltages across lenses 44 or 39 with the propertiming can selectively remove time separated m/z ions as the pulsed ionpacket traverses flight tube 42. Electrically floating flight tube 42inside electrode assembly 40 to accelerate ions to kilovolt potentialsallows operation of ion guide 16 and pulsing region 30 lenses withvoltages closer to ground potential. This lower voltage operationsimplifies design and lowers the cost of the control circuitry for theseelements.

Continuous Ion Beam Operation

When the API/TOF instrument diagrammed in FIG. 1 is operated in acontinuous beam mode, no break occurs in the ion beam between capillaryexit 12 and pulsing region 30. In this mode ions continuously to enterion guide 16. In one ion guide operating mode, the voltages applied toion guide 16, a quadrupole in the preferred embodiment shown, aregenerally set to RF or AC only. This is equivalent to operating alonga=0 line 101 of stability diagram 102 in FIG. 9. Ions enter traversealong the gap between lenses 34 and 35 when the relative voltage betweenlenses 34 and 35 is set at 0 V. Rapidly increasing the relative voltagebetween lenses 34 and 35 with the correct polarity accelerates ions inthe gap down flight tube 42 for mass analysis. The relative voltagebetween lenses 34 and 35 is then returned to zero and ions travelingthrough lens 28 begin to refill the pulsing region gap 30 between lenses34 and 35. The TOF duty cycle for a given value of m/z is determined bya combination of the pulse rate down the flight tube, the fill time of,pulsing region 30 and the ion flight time through the TOF flight tube42. For example, if a flight time of m/z 5,000 is 100 μsec, then themaximum pulse rate would be 10 KHz to avoid the lower m/z ions of thenext pulse from overtaking the heavier m/z ions of the first pulse inthe TOF tube before the point of impact with detector 38 or 47. If thetime for an ion of a given m/z value to fill the useable portion ofpulsing region 30 is shorter than 100 μsec then a portion of these m/zvalue ions will travel past the pulsing region and be lost, reducing theduty cycle for that value of m/z. As examples; a 10 ev ion of m/z 5,000will fill the pulsing region sweet spot in approximately 67 μsec and anof m/z 500 in approximately 12 μsec. Only a portion of the ions fillingthe gap between lenses 34 and 35 will actually make it into the flighttube when the voltages on lenses 34 and 35 are pulsed, the duty cyclesfor m/z ions 5,000 and 500 are 32% and 7% respectively. The m/z range ofprimary ion beam 48 can be reduced by setting AC and DC voltagesamplitudes to establish the appropriate a and q values which willachieve stable trajectories on ions through the multipole ion guide forthe desired m/z range. In this manner the pulse rate can be increased,improving duty cycle without overlapping high and low m/z ions in theTOF flight tube. Due to constraints imposed by circutiry, factors ofonly 2 to 4 can be gained by increasing the TOF rat; consequently, m/z500 may only achieve a maximum duty cycle of 28% in continuous beamoperating mode. Instead, trapping and the timed release of ions from themultipole ion guide is a preferred method for improving duty cycle.

Trapping of ions in the multipole ion guide with subsequent release ofions into pulsing region 30 can be achieved by of two methods. Due tocollisional cooling of ions with the neutral background gas particularlyin the high pressure region at entrance region 60 of ion guide 16 shownin FIG. 2, the kinetic energy of ions traversing the ion guide isgreatly reduced from the energy spread of ions which exit skimmerorifice 13. Typically the total ion energy spread for ions leaving ionguide 16 after a single pass is less than 1 ev over a wide range of m/zvalues. Due to this kinetic energy collisional damping, the averageenergy of ions in ion guide 16 becomes common DC offset potentialapplied equally to all ion guide rods 20. For example, if ion guide 16has an offset potential of 10 ev relative to ground, then the ionsexiting ion guide 16 at exit end 24 will have an average ion energy ofapproximately 10 ev relative to ground potential. FIG. 2 shows anenlargement of multipole ion guide 16 and pulsing region 30. The firstand simplest way to trap ions in ion guide 16 is by raising the voltageapplied to lens 26 high enough above the offset potential applied to ionguide 16 to insure that ions are unable to leave the ion guide RF fieldat exit end 24 and are reflected back along ion guide 16 towardsentrance end 60. The voltage applied to skimmer 14 is set higher thanthe ion guide offset potential to accelerate and focus ions into the ionguide. Consequently, ions traveling back from exit end 24 towardsentrance end 60 are rejected from leaving the exit end by the higherskimmer potential and the neutral gas stream flowing through skimmerorifice 13 into entrance end 60 of ion guide 16. In this manner, ions 50with m/z values that fall within the ion guide stability window aretrapped in ion guide 16. Ions are released from the ion guide bylowering the voltage on lens 26 for a short period of time and thenraising the voltage to trap the remaining ions in ion guide 16. Thedisadvantage of this simple trapping and release sequence is thatreleased ions that are still between lens 26 and 27 are accelerated topotentials higher that the average ion energy when the voltage on lens26 is raised. These higher energy ions are effectively lost.

A second method to achieve more efficient trapping and release is tomaintain the relative voltages between capillary exit 12, skimmer 14 andoffset potential of ion guide 16 constant. With the relative voltagesheld constant, all three voltages are dropped relative to the lens 26voltage to trap ions within ion guide 16. Capillary 7 as diagrammed inFIG. 1 is fabricated of a dielectric material and the entrance and exitpotentials are independent as is described in U.S. Pat. No. 4,542,293.Consequently, the exit potential of capillary 7 can be changed withouteffecting the entrance voltage. In this manner, the ions which arereleased from ion guide 16 by simultaneously raising voltages oncapillary exit 12, skimmer 14 and the offset potential of ion guide 16and these ions pass through lens 26 retaining a small energy spread andremain optimally focused into pulsing region 30. After a short timeperiod the three voltages are lowered to retain trapped ions within ionguide 16. A large portion of the released ions between lenses 26 and 27are unaffected when the offset potential of ion guide 16 is lowered totrap ions remaining in the ion guide internal volume.

By either trapping method, ions continuously enter ion guide 16 evenwhile ion packets are being pulsed out exit end 24. The time duration ofthe ion release from ion guide exit 24 will create an ion packet 52 of agiven length as diagrammed FIG. 2. As this ion packet moves throughlenses 27 and into pulsing region 30 some m/z TOF partitioning can occuras diagrammed in FIG. 3. The m/z components of ion packet 52 can occupydifferent axial locations in pulsing region 30 such as separated ionpackets 54 and 56 along the primary ion beam axis. Separation hasoccurred due to the velocity differences of ions of different m/z valueshaving the same energy. The degree of m/z ion packet separation is tosome degree a function of the initial pulse duration. The longer thetime duration that ions are released from exit 24 of ion guide 16, theless m/z separation that will occur in pulsing region 30. All or aportion of ion packet 52 may fit into the sweet spot of pulsing region30. Ions pulsed from the sweet spot in pulsing region 30 will impinge onthe surface of detector 38. If desired, a reduced m/z range can bepulsed down flight tube 42 from pulsing region 30. This is accomplishedby controlling the length of ion packet 52 and timing the release of ionpacket 52 from ion guide 16 with the TOF pulse of lenses 34 and 35. Atime separated m/z ion packet consisting of subpackets 54 and 56 justbefore the TOF ion pulse occurs is diagramed in FIG. 3. Ion subpacket 56of lower m/z value has moved outside the sweetspot and will not hit thedetector when accelerated down flight tube 42. Ion subpackets 57,originally subpackets 54, are shown just after the TOF ion pulse occurs.These subpackets will successfully impinge on detector 38. The longerthe initial ion packet 52 the less mass range reduction can be achievedin pulsing region 30. With ion trapping in ion guide 16, high dutycycles can be achieved and some degree of m/z range control in TOFanalysis can be achieved independent or complementary to mass rangeselection operation with ion guide 16. The ion fill level of multipoleion guide 16 operated in trapping mode is controlled by the ion fillrate, stable m/z range selected, the empty rate set by the ion guide ionrelease time per TOF pulse event and the TOF pulse repetition rate.During continuous ion guide filling, m/z selective CID fragmentation canbe performed within ion guide 16, with high duty cycle TOF massanalysis.

CID Fragmentation with Continuous Ion Beam Operation

As was described in the above sections, a resonant frequency of lowamplitude voltage can be added to the primary AC voltages applied torods 20 of multipole ion guide 16. If the voltage amplitude of theapplied resonant frequency applied is high enough, it will cause the m/zvalue with that resonant frequency in quadrupole 16 to be ejectedradially from ion guide 16 before reaching exit end 24. This is onemethod of achieving ion guide/TOF m/z range selection in trapping or nontrapping ion guide operation. If the same resonant frequency is appliedwith a reduced amplitude, selective m/z ion CID with the neutralbackground gas can be achieved for the selected m/z values as the ionspass through or are trapped in ion guide 16. Several ions may be presentin the parent mass spectrum, however, only the ion with an m/z valuewhich corresponds to the selected resonant frequency will undergoresonant frequency excitation CID fragmentation. The resulting fragmentions resulting from the parent ion resonant excitation CID can beidentified by subtraction of a previously acquired mass spectrum with noCID fragmentation. As an example, say the TOF pulse repetition rate is10 KHz and 1000 of the large mass range individual TOF mass spectracreated per pulse will be added to form a summed mass spectrum. In thismanner 10 summed mass spectra will be saved per second. During the 0.1sec acquisition time of each even numbered summed mass spectrum, theresonant frequency which corresponds to say m/z of 850, the ion ofinterest, is added to the AC component applied to rods 20 of ion guide16. The amplitude of this resonant frequency voltage component is highenough to cause CID fragmentation of m/z 850 due to ion collisions withthe neutral background gas but not so high as to cause an unstabletrajectory and hence the rejection of m/z 850 from the ion guide. Theresonant frequency is then turned off for each odd numbered summed massspectrum acquired. Each odd numbered mass spectrum can then besubtracted its following even numbered mass spectrum resulting in asubtracted spectrum containing the fragment ions resulting from the CIDfragmentation and the difference in the parent peak height before andafter fragmentation. This continuous beam CID fragmentation techniqueprovides the equivalent information to a single MS/MS step with half theduty cycle of a non fragmentation experiment with or without ion guide16 operated in trapping mode. In non trapping mod; this method ofproducing first generation ion fragments minimizes unwanted ion-ion orion neutral reactions. Ions in non trapping mode take only a single passthrough the ion guide minimizing the number of collisions which couldpotentially result in reaction species which produce unknown massspectral peaks.

In a similar manner, a mass spectrum equivalent to an MS/MS² experimentstep can be acquired. In such an MS/MS² experiment, the goal is toproduce a mass spectrum of the second generation fragment ions resultingfrom CID fragmentation of a first generation fragment ion which itselfhas been produced by fragmentation of the parent. With conventionalMS/MS operation, the analysis steps would include;

-   1. m/z selection of the parent ion in trap mode,-   2. cause CID the fragmentation of the parent ion while trapping the    fragment ions produced,-   3, m/z selecting the first generation fragment ion of interest in    the ion guide trap,-   4, cause CID of the m/z selected first generation fragment ion and    trap the resulting second generation fragment ions, and-   5. produce a mass spectrum of the second generation fragment ions.

Similar MS/MS² results can be acquired using an extension of thetechnique described in the previous paragraph. In this case, ion guide16 can be operated in either trapping or non trapping mode withcontinuous filling. If the cascade fragmentation process requires moretime to complete than the time it takes for an ion to make a single passthrough the ion guide higher pressure region then the ion guide 16 canbe operated in trapping mode. Very high duty cycle can be maintained inion guide trapping mode with lower TOF pulse repetition rates. Thus thetrapped ions of interest have a longer residence time in the higherpressure region of ion guide 16 where CID can occur. To produce anMS/MS² mass spectrum, a set of two or three individual mass spectrum isacquired. In a set of three, the three individual mass spectra includeone full parent ion spectrum, one mass spectrum resulting from the CIDof the selected parent ion using resonant frequency excitation of theparent ion m/z value and one spectrum with simultaneous CID of theselected parent and first generation fragment ion using two frequenciesof resonant excitation, one for each of the two m/z values. With thisdata set, a mass spectrum of the first generation fragments can beproduced by subtracting the full parent mass spectrum from the singleresonant frequency excitation CID mass spectrum as was described in theprevious paragraph. A mass spectrum of the second generation fragmentscan be produced by subtracting the mass spectra acquired using thesingle resonant frequency excitation from the mass spectra acquiredusing the double resonant frequency excitation. If just the secondgeneration fragment mass spectrum were desired, the acquisition of onlytwo mass spectra would be required for subtraction and hence the dutycycle is only one half that of the optimal parent ion trapping mode ofoperation. If the fragmentation sequence is desired for MS/MS²acquisition then the duty cycle of the second generation fragment ionmass spectrum would be one third that of the optimal parent ion trappingmode of operation as three summed mass spectra would be acquired.Clearly this resonant frequency CID technique using a multipole ionguide with single or multiple resonant frequency CID fragmentation canbe extended to perform high duty cycle MS/MS^(n) analysis. Also severalfragments ions of a given ion fragment generation could be selectivelyfragmented and recorded in successive mass spectra to acquire extensiveion fragmentation maps for a given parent ion species. The energy of theselective CID process can be controlled to some degree by adjusting theinitial parent ion internal energy using the capillary to skimmerpotential. The TOF pulse rate is so rapid that several MS/MS^(n)experimental acquisition sequences can be acquired within a one secondtime frame. Thus one aspect of the invention enables the running of highsensitivity MS/MS^(n) experiments on line with fast separation systemssuch as perfusion LC or CE even where chromatographic peak widths ofless than one second are eluting.

CID Fragmentation with Interrupted Ion Beam Operation

In another aspect of the invention true mass selective MS/MS^(n)experiments can be performed using ion guide 16 with TOF mass analysis.In this experimental sequence, the ion beam entering the ion guide 16 atentrance end 60 is interrupted during the CID fragmentation step orsteps. The primary ion beam can be turned off by applying a repellingpotential between capillary exit 12 and skimmer 14 which prevents ionsexiting capillary 7 from entering skimmer orifice 13. With theembodiment of the invention as diagrammed in FIG. 1, an MS/MS experimentincludes the steps of m/z selection and accumulation in ion guide 16operating in trapping mode followed by an ion fragmentation step.Initially, in an MS/MS experiment, the primary ion beam is turned on andions enter ion guide 16 which is operating in m/z selection mode. Asdescribed above, mass or m/z selection in ion guide 16 can achieved in anumber of ways. One is by setting AC and DC voltage components on ionguide rods 20 resulting in operation near apex 100 stability diagram 102in FIG. 9. A second method is by operating ion guide 16 along the a=0line and applying resonant frequency rejection for all ions but theselected m/z value or values. A third method is to accumulate ions in RFonly mode and by adjusting AC and DC amplitudes, scan out all but them/z values of interest. When the multipole ion guide operating in trapmode has been filled to the desired level with the selected m/z range ofions, the primary ion beam is turned off preventing additional ions fromentering ion guide 16 at entrance 60. Fragmentation of trapped ions inion guide 16 can be achieved by, using one of at least three techniques.The first technique as was described above for continuous beam operationis to apply a resonant frequency to rods 20 of ion guide 16 to causeresonant excitation of all or a portion of the trapped ions. Theresonant excitation results in fragmentation due to CID of thetranslationally excited ions with the background gas in ion guide 16.

A second technique and another aspect of the invention allows higherenergy fragmentation to occur than can be achieved with resonantfrequency CID. This second ion fragmentation technique is realized byswitching the offset potential of ion guide 16 and the voltage appliedto lens 26 to release ions trapped in ion guide 16 and accelerating themat higher energy back into exit end 24. A short release pulse is usedsuch that ions leaving ion guide exit 24 move to fill the gap betweenlenses 26 and 27. When the gap between lenses 26 and 27 is filled, thevoltages on lenses 26 and 27 are rapidly increased effectively changingthe energy of ions in the gap between the end of rods 20 and lens 27.The relative voltages on the lenses 26 and 27 and the offset potentialof ion guide 20 are set such that the ions sitting at a raised potentialare accelerated back into the exit end 24 of ion guide 16 and travelfrom ion guide exit end 24 toward ion guide entrance end 60 through thelength of the internal volume of ion guide 16 colliding with neutralbackground molecules in a portion of the ion guide length. The iontraversing ion guide 16 in the reverse direction are prevented fromleaving entrance end 60 of ion guide 16 by setting the appropriateretarding potential on skimmer 14. During this step where ions areaccelerated back into ion guide exit 24, the ion guide offset potentialand the voltage on lens 26 are set such that ions within the ion guideremain trapped. One advantage of the multiple vacuum stage configurationof ion guide 16 is that ions are initially reverse accelerated back intoexit end 24 of ion guide 16 in a low pressure region with initially noion collisions occurring with the background gas. Consequently, the ionscan achieve higher velocities resulting in higher energy collisions whenthey encounter the higher pressure background gas closer to ion guideentrance 60. This ion reverse direction acceleration step can berepeated a few or several times to fragment a portion or all of theparent ions trapped in the ion guide. This repetitive reverse directionacceleration step can also cause additional fragmentation of fragmentions provided the collision energies are sufficient. After sufficiention fragmentation has occurred by this method, a series of TOF massspectra can be acquired of the ion population trapped in ion guide 16.As was described in an earlier section, releasing of trapped ions fromion guide 16 for TOF mass analysis followed by trapping of the ionsremaining in ion guide 16, can be achieved either by changing thevoltages on just lens 26 or conversely, the ion guide offset potential,skimmer 14 voltage and the voltage on capillary exit 12 can be steppedtogether.

Resonant frequency excitation of selected m/z values will can causefragmentation of those selected m/z values without causing fragmentationof unselected m/z values. The reverse direction acceleration ionfragmentation technique as described in the previous paragraph is notm/z selective and can cause fragmentation of any ion species which willfragment at the CID energy achieved in the reverse direction ionacceleration. The ion collisional energy in this reverse directionacceleration technique, however, can be finely controlled by therelative voltages set on lenses 26 and 27 and the offset potential ofion guide 16 during ion acceleration into exit end 24 of ion guide 16. Athird technique to fragment ions trapped in multipole ion guide 16 isanother aspect of the invention. It was found that when ion guide 16 isfilling with ions, a point is reached where fragmentation of the parention occurs. TOF mass spectra illustrating this ion CID technique areshown in FIG. 8 for Leucine Enkephalin with a molecular weight of 556for the protonated ion, TOF mass spectra were acquired using a TOF whichincluded a collinear pulsing region as diagrammed in FIGS. 6 and 7 and amultipole ion guide operated in ion trapping mode. Mass spectrum 80 wasacquired with a capillary to skimmer relative voltage of 97 volts and anion guide fill time of 0.5 seconds before the primary ion beam was cutoff and the TOF mass spectrum was acquired. No appreciable fragmentationwas observed with these conditions even if ions remained trapped forsome time before releasing a series of ion packets to acquire TOF massspectra. Prior to the acquisition of TOF mass spectrum 82, the ion guidefill time was increased to 1.65 seconds retaining the capillary toskimmer relative voltage at 97 volts. As can be seen from the acquiredTOF mass spectrum 82, fragmentation of the protonated Leucine Enkephalinion has occurred. Raising the capillary to skimmer potential increasesthe internal energy of the ions entering the ion guide. With higherrelative capillary to skimmer voltage applied, less additional energy isthen required to fragment the more highly energetic Leucine Enkephalinparent ions in the ion guide. This is observed in TOF mass spectrum 81where the relative capillary to skimmer potential was increased to 187volts and fragmentation of the Leucine Enkephalin ion occurred at only0.5 seconds of ion guide fill time.

The precise mechanism of this fragmentation process is not completelyunderstood but evidence from related experiments suggests that reversedirection ion acceleration into ion guide exit end 63 as was describedin the previous paragraph may play a role. It was found that as the ionguide fills with ions, the space charge repulsion of ions trapped withinion guide 60 caused a portion of the ions trapped within ion guide 60 tobulge into the gap between exit end 63 and lens 64. For the dataacquired in FIG. 8, the ion guide offset potential was set at 10 ev andthe trapping potential applied to ion guide exit lens 64 was positive 40volts. Thus, ions which are bulging into the gap between ion guide exit63 and lens 64 have a potential which falls between 10 and 40 ev. Thesehigher energy ions are accelerated back into ion guide exit 63 andtraverse the length of ion guide 60 where they collide with neutral gasbackground molecules within ion guide 60. Parent ion fragmentation doesnot occur until the energy of collision is sufficiently high to breakthe weakest bond. As ion guide 60 fills with ions, increased spacecharge bulges the ions further out into the increasingly higherelectrostatic fields in the gap between ion guide exit 63 and lens 64.Due to this effect, ions accelerated back into ion guide 60 through exit63 have increasing energy as the ion guide fills. It is not yet certainwhat role the ion guide fringing fields play in the ion fragmentationprocess resulting from filling ion guide 60. It should be noted thateach TOF mass spectrum 80, 81 and 82 shown in FIG. 8 is the summation of5 individual TOF mass spectrum. The ion release from ion guide 60, wasachieved by rapidly lowering the potential on lens 64 to minus 40 volts.The voltage on lens 64 was dropped from plus 40 to minus 40 volts inless than 50 nanoseconds, held at minus 40 volts for 5 μsec, thenreturned to plus 40 volts with a rise time of less than 50 nanoseconds.The signal ringing 85 in the mass spectra of FIG. 8 is from the fallingedge of the lens 64 voltage pulse and the ringing at point 86 is causedby the rising edge. Both of these ringing events occur before the lowestm/z ions hit detector 71 so the mass spectrum is not effected by thiselectronic related noise. A point to note is that the total ion releasetime from ion guide 60 is 5 μsec for each individual TOF spectraacquisition. Five individual TOF mass spectra were summed to produceeach mass spectra shown in FIG. 8. Hence a total of 25 μsec of ion guidetrap empty time was required to produce each parent and first generationfragment ion mass spectra 80, 81 and 82 respectively. Similar, ionsignal levels were obtained for ions trapped in ion guide 60 over an ionrelease period exceeding 200 μsec. Consequently, several summed TOF massspectra can be produced from one set of ions trapped in ion guide 60.The ion guide can trap ions with little or no loss over a time period ofseveral minutes.

The ability to acquire summed mass spectra from only a portion of theions trapped within ion guide 60 or ion guide 16 creates the ability toacquire TOF mass spectra data for several experiments using the same setof ions. One application for this capability would be to capture fastevents occurring from an on line separation system. If a peak elutedfrom an on line CE column in less than 0.5 seconds, the Electrospraygenerated ions resulting from the sample eluting in the peak could becaptured by trapping them in ion guide 16. After capturing samplerelated ions generated from the CE peak, the primary ion beam could beturned off and several experiments could be run on the ion set eitherunder preset instrument control or by user selected functions. A seriesof experiments run on a trapped set of ions could be as follows. Asummed TOF mass spectra is first acquired to record the parent ionspresent. From the data acquired, the user selects a parent m/z ofinterest and fragments this ion by selective resonant frequencyexcitation. A summed TOF mass spectrum is acquired and it is subtractedfrom the first mass spectrum to obtain a fragment ion mass spectrum. Asecond parent ion m/z value is selected using the first mass spectrumand fragmentation is achieved through selected resonant frequencyexcitation of the second parent ion m/z. The resulting third summed massspectra is subtracted from the second to obtain the set of fragment ionswhich resulted from the second parent ion. The fourth experiment mightbe to clear the trap of all but one m/z by resonant ejection andfragment the remaining trapped ions using high energy CID using thetechnique described above where ions are reverse direction acceleratedback into ion guide exit 24. An MS/MS² experiment can then be run on aresulting high energy CID fragment. As this example illustrates, manytypes and combinations of experiments can be run on a single set oftrapped ions with multiple TOF spectra generated. If a series ofexperiments were preset and repetitive, several experiments could beconducted on each ion set trapped automatically during an on lineseparation or with multiple samples run in a repetitive flow injectionanalysis. Due to the rapid acquisition capability of the TOF massanalyzer, a complex sequence of experiments can be run and several TOFmass spectra recorded for a set of trapped ions in a time period of lessthan one second. By adding a selected reactant gas into vacuum stages 18or 19 in FIG. 1, gas phase reactions with trapped ions can be studied aswell with the techniques described above. For example, the substitutionof deuterium for hydrogen in trapped protonated ions of proteins tostudy the gas phase folding structure can be monitored in this manner.

An MS/MS experiment using the apparatus as diagrammed on FIG. 1 can haveseveral variations as described in the above sections due to theoptional techniques available to achieve each functional step. Whenoperating where the primary ion beam is shut off between ion guidefilling cycles, a typical MS/MS experimental may include the followingsequence of steps;

-   1. The primary ion beam is turned on and ions fill the ion guide    which is operated in ion selection trapping mode,-   2. After a period of trap fill time, the beam is shut off,-   3. The ion guide rod voltages are set for wide in/z range trapping    mode operation,-   4. A TOF mass spectrum is acquired of the trapped parent ion from a    portion of the ions trapped in the ion guide,-   5. Fragment ions are produced in the ion guide trap from the    remaining trapped parent ions,-   6. One or more TOF mass spectra are acquired of the resulting    trapped ions.-   7. The ion guide is emptied of all remaining ions,-   8. Steps 1 through 7 are repeated.

Step four can be eliminated in the sequence given above if rapid MS/MSTOF acquisition is required. A widely used MS/MS triple quadrupoleexperiment termed neutral loss or multiple reaction monitoring (MRM) isaccomplished by scanning quadrupole three simultaneously with quadrupoleone maintaining a set m/z offset between the two quadrupoles. Ionspassing through quadrupole one are fragmented by CID in quadrupole two.Any fragment ion with the preset m/z offset from the parent ion m/z willpass through quadrupole three and be recorded. Emulation of a triplequadrupole neutral loss or MRM experiment can be achieved with the APITOF configuration as diagrammed in FIG. 1 operated in MS/MS mode. Anexample will be used to describe this capability. Say a triplequadrupole MRM scan is taken over a parent ion mass range from 200 to1,000 m/z in two seconds. To maximize sensitivity and include parentisotope peaks, quadrupole one passes an m/z window of four m/zthroughout its scan. To emulate this triple quadrupole function, theAPI/multipole ion guide/TOF is operated in the following manner. The ionguide is operated in mass selective non continuous ion beam trappingMS/MS mode where a four m/z stability window is selected. Eachindividual TOF mass spectrum is acquired at a rate of 1,000 Hertz withevery ten individual TOF mass spectra added to produce a saved TOF massspectra. In this manner 100 added TOF mass spectra will be saved persecond. Two trap fill MS/MS cycles are performed per added mass spectrumwith 5 individual TOF mass spectrum acquired from each MS/MS cycle.After every ten individual TOF mass spectra or one added mass spectra,are acquired, the selected trapped m/z range is shifted up by four m/z.In this manner 100 MS/MS experiments are conducted over a 400 m/z rangein a 4 m/z per MS/MS cycle stepwise fashion. An 800 m/z range can becovered in 2 seconds emulating the triple quadrupole MRM example givenabove. The resulting TOF data set is not restricted to just a singlescan of a selected offset ion as in the triple quadruple case butcontains 200 full mass spectra of all the fragment ions produced per m/zwindow trapped. The triple quadrupole MRM experiment is only onespecific selected ion chromatogram extracted from 200 TOF mass spectra.With the emulated TOF MRM acquisition far more analytically usefulinformation is available than is the case with the triple quadrupoleacquisition. An analogous MRM simulated experiment can be performed bythe API TOF instrument in the continuous ion beam operating mode as wellwith or without trapping.

The sequence described in the previous paragraph is one example of howthe MS/MS^(n) API TOF capability as described in the invention can beutilized either on line with a separation system or when analyzinglimited sample amounts. The API TOF instrument can be set up to acquiremass spectral data while rapidly performing a complex sequence ofMS/MS^(n) experiments. In this manner a large data set is acquired usingvery little sample. A range of simulated experiments can then be run onthe data set only by grouping or extracting various portions of theacquired data set without consuming additional sample.

An MS/MS² experiment can be run with the apparatus diagrammed in FIG. 1by extending the number of steps used in the MS/MS experiment asfollows;

-   1. The primary ion beam is turned on and ions fill the ion guide    which is operated in ion selection trapping mode,-   2. After a period of trap fill time, the beam is shut off,-   3. The ion guide rod voltages are set for wide m/z range trapping    mode operation,-   4. Fragment ions are produced in the ion guide trap from the    remaining trapped parent ions,-   5. A second m/z range of ions is selected which includes a first    generation fragment ion and all ions not in the selected m/z value    range are rejected from the ion guide,-   6. The ion guide rod voltages are reset for a wide m/z range    trapping mode operation,-   7. Fragment ions are produced in the ion guide trap from the    remaining first generation fragment ions,-   8. One or more TOF mass spectra are acquired from the resulting    trapped ions,-   9. After TOF acquisition, the ion guide is emptied of all remaining    ions,-   10. Steps 1 through 10 are repeated.

MS/MS^(n) experiments can be run by repeating steps 5, 6 and 7 asdescribed in the MS/MS² sequence above for higher generation fragmentions for the desired number times to create the desired n generationfragment ions. TOF mass spectra may be acquired after one or moreselected fragmentation steps in an MS/MS^(n) experiment using only aportion of ions trapped in ion guide 16. Several variations insequencing functional steps to achieve MS/MS^(n) analytical capabilityare possible in addition to those described above.

Alternative embodiments of the invention are diagrammed in FIGS. 4, 5, 6and 7. The ion guide and TOF pulsing region of a four vacuum stage APIorthogonal pulsing TOF mass analyzer is diagrammed in FIG. 4. Themultiple vacuum pumping stage ion guide shown in FIG. 1 has beenreplaced by two multipole ion guides each of which begins and endswithin one vacuum pumping stage. Multipole ion guide 110 is locatedentirely in the second vacuum pumping stage 112. A second multipole ionguide 111 is located entirely in the third vacuum pumping stage 113.Electrostatic lens 114 positioned between ion guides 110 and 111 servesas a vacuum stage partition between vacuum stages 112 and 113 and as anelectrostatic ion optic element separating ion guides 110 and 111. Ionsproduced in an API source enter the first vacuum stage 117 throughcapillary exit 116. A portion of these ions continue through skimmerorifice 118 and enter multipole ion guide 110. Operating in single passcontinuous beam mode, ions pass through ion guide 110, lens orifice 115,ion guide 111 and into TOF orthogonal pulsing region 120 where they arepulsed into TOF tube 123 and mass analyzed. Ion guide 110 operates in abackground pressure typically maintained between 5×10⁻⁴ and 1×10⁻² torr.Ion guide 111 operates in a background pressure maintained typicallybelow 1×10⁻³ torr. Ion transfer between ion guides 110 and 11 andelectrostatic lens 114 may not be as efficient as that achieved with amultiple vacuum stage multipole ion guide as shown in FIG. 1 but somesimilar MS/MS^(n) functional capability can be achieved with theembodiment diagrammed in FIG. 4. In the configuration shown in FIG. 4ion guide 110 can be operated in trapping mode. Due to the higherpressure in ion guide 110 and using techniques such as resonantfrequency excitation, ion fragmentation can occur due to CID of ionswith the neutral background gas within ion guide 110. Voltages can beapplied independently to ion guides 110 and 111, so both ion guides canbe operated in variety of trapping or transmission modes with differentoffset potentials or m/z selection. This operational flexibility allowssome variation in functional step sequences in acquiring MS/MS^(n) datafrom those described for the embodiment illustrated in FIG. 1.

For example, a variation can be used with the embodiment shown in FIG. 4to achieve the equivalent capability as was described with the reversedirection acceleration ion fragmentation technique described for theapparatus diagrammed in FIG. 1. With the two ion guide configurationshown in FIG. 4, ion guide 110 can be operated in a wide m/z rangetrapping mode and ion guide 111 in a m/z selective trapping mode. Thetrapped ions in ion guide 111 can be accelerated back into ion guide 110through lens orifice 115 by increasing the offset voltage of ion guide111 relative to the offset potential of ion guide 110. Ions traversingion guide 110 moving in the reverse direction towards entrance end 124,collide with neutral background molecules. In this manner m/z selectiveion fragmentation with higher energy CID can be achieved. A secondexample of a function variation using the embodiment shown in FIG. 4creates the ability to perform selected ion-ion reaction monitoring. Toperform this analysis, both ion guides are operated in trapping modewith different m/z range selection chosen for each ion guide. Afragmentation experiment can be run in ion guide 110 without changingthe ion population in ion guide 111. The different ion populations fromboth in guides can then be recombined by acceleration of ions from oneion guide into the other to check for ion reactions before acquiring TOFmass spectra of the mixed ion population. The ion guide m/z selectionand ion fragmentation techniques described in previous sections can beapplied to multipole ion guide embodiment shown in FIG. 4 to achievemost of the equivalent and even some additional MS/MS^(n) analysisperformance capability.

Another embodiment of the invention is shown in FIG. 5 which is adiagram of the multipole ion guide and orthogonal TOF pulsing region ofa three vacuum pumping stage API TOF mass analyzer. In this embodiment,a portion of the ions exiting capillary exit 130 are focused throughskimmer orifice 131 and enter multipole ion guide 132. The pressure inthe second vacuum pumping stage 138 is maintained at a level where ionfragmentation by CID with the background gas is possible using the ionfragmentation techniques described in the previous sections. Generallythis will require a background pressure in vacuum stage 138 higher than5×10⁻⁴ torr. With the apparatus diagrammed in FIG. 5, MS/MS^(n)functional capability as described above for the apparatus diagrammed inFIG. 1 can be realized. However, the higher background pressure found atexit end 139 of ion guide 132 may not be optimal to achieve collisionfree ion focusing and beam shaping through lenses 134 and 135 and intoTOF pulsing region 136. Depending on the background pressure level, thehigher pressure at ion guide exit lens 139 may also effect theperformance of the ion fragmentation technique which uses ionacceleration back into ion guide exit 139 to achieve ion CID in ionguide 132. One disadvantage to using the apparatus diagrammed in FIG. 5is that as the background pressure in vacuum stage 138 is increased toachieve more efficient CID in ion guide 132, it becomes increasinglydifficult to maintain low vacuum pressure in the TOF tube 137. Thepressure in vacuum stage 140 can be reduced by increasing the vacuumpumping speed but this increases vacuum pump cost and potentiallyincreases the instrument size. The neutral gas conductance between thesecond and third vacuum stages 138 and 140 respectively can be reducedby decreasing the size of orifice 141 in lens 134. However, reducing thesize of orifice 141 may have the negative effect of reducing the iontransmission through lenses 134 and 135 leading to TOF orthogonalpulsing region 136. One advantage to the three vacuum pumping stageconfiguration shown in FIG. 5 is that potentially fewer vacuum stagesresults in lower instrument cost.

An alternative embodiment of the invention is shown in FIGS. 6 and 7. Afour vacuum pumping stage API TOF mass analyzer is diagrammed in FIG. 6which includes a TOF pulsing region oriented collinear with themultipole ion guide axis. The configuration shown in FIG. 6 from theElectrospray ion source 74 through ion guide 60 to electrostatic lens 66is essentially the same apparatus and has the same functionality as theregion described in FIG. 1 from Electrospray ion source 1, through ionguide 16 to electrostatic lens 27. Hence several of the MS/MS^(n)analysis functions can be performed with the apparatus diagrammed inFIG. 6 in a manner similar to that described above for the apparatusshown in FIG. 1. One primary difference with the collinear pulsingconfiguration shown in FIG. 6 is that ion guide 60 must always beoperating in trapping mode and the ion release pulse length can not bevaried without effecting the TOF mass analysis. Only a short durationion release pulse from ion guide 60 can be used with the collinear TOFpulsing geometry. Increasing the duration of the ion release pulse fromion guide 60 decreases TOF analysis resolution. Some degree of DC lenstrapping can be achieved after lens 64 as described by Boyle et. al,(Rapid Commun. Mass Spectrom. 1991, 5, 4000), however, even DC trappingmay be inadequate to compensate for the long times required to extracthigher m/z value ions from ion guide 60. With shorter duration ionrelease pulses from ion guide 60 relative m/z transmissiondiscrimination can occur. A larger number of lower m/z value ions can bereleased from ion guide exit end 63 per time due to their faster ionvelocity when compared to higher m/z values in short duration pulses.Consequently, the relative m/z ion population of a TOF ion packet pulseddown flight tube 70 may differ from the relative m/z ion populationtrapped in ion guide 60 when short duration ion release pulses are used.Also with the constraint that only short duration release pulses can beused to extract ions from ion guide 60, the level of ion guide fillingis more difficult to control without shutting off the primary beam.Interrupting the primary beam reduces the effective duty cycle. Anotherfeature of the collinear TOF pulsing geometry is that all ions thatleave ion guide 60 are pulsed down flight tube 70. There is no componentof primary beam Time-Of-Flight m/z separation before the TOF pulse as isfound in orthogonal TOF pulsing when short duration ion release pulsesare used. This performance feature of the collinear TOF pulsing geometrymay be an advantage or a disadvantage depending on the analyticalapplication. Alternatively, TOF tube 70 may include an ion reflector.

Although the invention has been described in terms of specific preferredembodiments, it will be obvious and understood to one of ordinary skillin the art that various modifications and substitutions are includedwithin the scope of the invention as defined in the appended claims. Inaddition, various references relevant to the disclosure of the presentapplication are cited above, and are hereby incorporated herein byreference.

What is claimed is:
 1. A method, comprising: directing ions from anatmospheric pressure ion source to a first ion guide; directing ions inthe first ion guide to a second ion guide, the second ion guide being amultipole ion guide extending along an axis; periodically directing ionsalong the axis; receiving at least some of the ions in a time-of-flightmass analyzer; accelerating the ions in the time-of-flight mass analyzerorthogonal to the axis; and detecting the accelerated ions, wherein thesecond ion guide is positioned between the first ion guide and thetime-of-flight mass analyzer.
 2. The method of claim 1, wherein the ionsare continuously directed from the atmospheric pressure ion source tothe first ion guide.
 3. The method of claim 1, wherein the ions areperiodically directed to the time-of-flight mass analyzer by trappingions within one of the ion guides.
 4. The method of claim 3, wherein theions are trapped in the second ion guide.
 5. The method of claim 1,further comprising fragmenting ions from the atmospheric pressure ionsource and directing the fragmented ions to the time-of-flight massanalyzer.
 6. The method of claim 5, wherein the ions are fragmented inthe first ion guide.
 7. The method of claim 1, further comprising massfiltering ions from the atmospheric pressure ion source before directingthe ions to the time-of-flight mass analyzer.
 8. The method of claim 7,wherein the ions are mass filtered using the second ion guide.
 9. Themethod of claim 1, wherein the first ion guide is located entirelywithin a first vacuum chamber and the second ion guide is locatedentirely within a second vacuum chamber portioned from the first vacuumchamber.
 10. The method of claim 9, further comprising maintaining abackground gas pressure in the second vacuum chamber below 1×10⁻³ ton.11. The method of claim 10, further comprising maintaining a backgroundgas pressure in the first vacuum chamber between 5×10⁻⁴ ton and 1×10⁻²torr.